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Watkins LC, DeGrado WF, Voth GA. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J Am Chem Soc 2020; 142:17425-17433. [PMID: 32933245 PMCID: PMC7564090 DOI: 10.1021/jacs.0c06419] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Prevalent resistance to inhibitors
that target the influenza A
M2 proton channel has necessitated a continued drug design effort,
supported by a sustained study of the mechanism of channel function
and inhibition. Recent high-resolution X-ray crystal structures present
the first opportunity to see how the adamantyl amine class of inhibitors
bind to M2 and disrupt and interact with the channel’s water
network, providing insight into the critical properties that enable
their effective inhibition in wild-type M2. In this work, we examine
the hypothesis that these drugs act primarily as mechanism-based inhibitors
by comparing hydrated excess proton stabilization during proton transport
in M2 with the interactions revealed in the crystal structures, using
the Multiscale Reactive Molecular Dynamics (MS-RMD) methodology. MS-RMD,
unlike classical molecular dynamics, models the hydrated proton (hydronium-like
cation) as a dynamic excess charge defect and allows bonds to break
and form, capturing the intricate interactions between the hydrated
excess proton, protein atoms, and water. Through this, we show that
the ammonium group of the inhibitors is effectively positioned to
take advantage of the channel’s natural ability to stabilize
an excess protonic charge and act as a hydronium mimic. Additionally,
we show that the channel is especially stable in the drug binding
region, highlighting the importance of this property for binding the
adamantane group. Finally, we characterize an additional hinge point
near Val27, which dynamically responds to charge and inhibitor binding.
Altogether, this work further illuminates a dynamic understanding
of the mechanism of drug inhibition in M2, grounded in the fundamental
properties that enable the channel to transport and stabilize excess
protons, with critical implications for future drug design efforts.
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Affiliation(s)
- Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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2
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Pham T, Nguyen HL, Phan-Toai T, Nguyen H. Investigation of Binding Affinity between Potential Antiviral Agents and PB2 Protein of Influenza A: Non-equilibrium Molecular Dynamics Simulation Approach. Int J Med Sci 2020; 17:2031-2039. [PMID: 32788882 PMCID: PMC7415388 DOI: 10.7150/ijms.46231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
The PB2 protein of the influenza virus RNA polymerase is a major virulence determinant of influenza viruses. It binds to the cap structure at the 5' end of host mRNA to generate short capped RNA fragments that are used as primers for viral transcription named cap-snatching. A large number of the compounds were shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, their binding in the context of an extended form of the PB2 protein has remained elusive. A previous study reported some promising compounds including azaindole and hydroxymethyl azaindole, which were analyzed here to predict binding affinity to PB2 protein using the steered molecular dynamics (SMD) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods. The results show that the rupture force (Fmax) value of three complexes is in agreement with the binding free energy value (ΔGbind) estimated by the MM-PBSA method, whereas for the non-equilibrium pulling work (Wpull) value a small difference between A_PB2-4 and A_PB2-12 was observed. The binding affinity results indicate the A_PB2-12 complex is more favorable than the A_PB2-4 and A_PB2-16 complexes, which means the inhibitor (12) has the potential to be further developed as anti-influenza agents in the treatment of influenza A.
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Affiliation(s)
- Tri Pham
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Tuyn Phan-Toai
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
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3
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Li Y, Lin Z, Guo M, Zhao M, Xia Y, Wang C, Xu T, Zhu B. Inhibition of H1N1 influenza virus-induced apoptosis by functionalized selenium nanoparticles with amantadine through ROS-mediated AKT signaling pathways. Int J Nanomedicine 2018; 13:2005-2016. [PMID: 29662313 PMCID: PMC5892959 DOI: 10.2147/ijn.s155994] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction As a therapeutic antiviral agent, the clinical application of amantadine (AM) is limited by the emergence of drug-resistant viruses. To overcome the drug-resistant viruses and meet the growing demand of clinical diagnosis, the use of biological nanoparticles (NPs) has increased in order to develop novel anti-influenza drugs. The antiviral activity of selenium NPs with low toxicity and excellent activities has attracted increasing attention for biomedical intervention in recent years. Methods and results In the present study, surface decoration of selenium NPs by AM (Se@AM) was designed to reverse drug resistance caused by influenza virus infection. Se@ AM with less toxicity remarkably inhibited the ability of H1N1 influenza to infect host cells through suppression of the neuraminidase activity. Moreover, Se@AM could prevent H1N1 from infecting Madin Darby Canine Kidney cell line and causing cell apoptosis supported by DNA fragmentation and chromatin condensation. Furthermore, Se@AM obviously inhibited the generation of reactive oxygen species and activation of phosphorylation of AKT. Conclusion These results demonstrate that Se@AM is a potentially efficient antiviral pharmaceutical agent for H1N1 influenza virus.
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Affiliation(s)
- Yinghua Li
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhengfang Lin
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Min Guo
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Mingqi Zhao
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yu Xia
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Changbing Wang
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tiantian Xu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Bing Zhu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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4
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Binding affinity of the L-742,001 inhibitor to the endonuclease domain of A/H1N1/PA influenza virus variants: Molecular simulation approaches. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Barniol-Xicota M, Gazzarrini S, Torres E, Hu Y, Wang J, Naesens L, Moroni A, Vázquez S. Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. J Med Chem 2017; 60:3727-3738. [PMID: 28418242 DOI: 10.1021/acs.jmedchem.6b01758] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
New insights on the amantadine resistance mechanism of the V27A mutant were obtained through the study of novel, easily accessible 4-(1- and 2-adamantyl)piperidines, identified as dual binders of the wild-type and V27A mutant M2 channels of influenza A virus. Their antiviral activity and channel blocking ability were determined using cell-based assays and two-electrode voltage clamp (TEVC) technique on M2 channels, respectively. In addition, electrophysiology experiments revealed two interesting findings: (i) these inhibitors display a different behavior against the wild-type versus V27A mutant A/M2 channels, and (ii) the compounds display antiviral activity when they have kd equal or smaller than 10-6 while they do not exhibit antiviral activity when kd is 10-5 or higher although they may show blocking activity in the TEV assay. Thus, caution must be taken when predicting antiviral activity based on percent channel blockage in electrophysiological assays. These findings provide experimental evidence of the resistance mechanism of the V27A mutation to wild-type inhibitors, previously predicted in silico, offer an explanation for the lack of antiviral activity of compounds active in the TEV assay, and may help design new and more effective drugs.
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Affiliation(s)
- Marta Barniol-Xicota
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Sabrina Gazzarrini
- Department of Biosciences and National Research Council (CNR) Biophysics Institute (IBF), University of Milan , Via Celoria 26, 20133 Milan, Italy
| | - Eva Torres
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona , Tucson, Arizona 85721, United States.,BI05 Institute, The University of Arizona , Tucson, Arizona 85721, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona , Tucson, Arizona 85721, United States.,BI05 Institute, The University of Arizona , Tucson, Arizona 85721, United States
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven , B-3000 Leuven, Belgium
| | - Anna Moroni
- Department of Biosciences and National Research Council (CNR) Biophysics Institute (IBF), University of Milan , Via Celoria 26, 20133 Milan, Italy
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona , Av. Joan XXIII, 27-31, Barcelona E-08028, Spain
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6
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Li Y, Lin Z, Zhao M, Guo M, Xu T, Wang C, Xia H, Zhu B. Reversal of H1N1 influenza virus-induced apoptosis by silver nanoparticles functionalized with amantadine. RSC Adv 2016. [DOI: 10.1039/c6ra18493f] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reversal of H1N1 influenza virus-induced apoptosis by silver nanoparticles functionalized with amantadine.
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Affiliation(s)
- Yinghua Li
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Zhengfang Lin
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Mingqi Zhao
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Min Guo
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Tiantian Xu
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Changbing Wang
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Huimin Xia
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
| | - Bing Zhu
- Center Laboratory
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou
- P. R. China
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